Process running on my atom causes the CPU to max at 100% on the server where the atom resides.
The atom is a java application. A java application will get/use as much CPU as it can/needs. Consequently, there is no way to limit the amount of CPU that the atom will consume. If you are concerned that the atom may interfere with other processing because of this fact, there are monitoring tools that can utilize that send alerts if a particular process passes a user configurable threshold.